Example class schedule
Biol 244 Genomics: Schedule
Date
M 8/31
W 9/2
Th 9/3
OH203
Topic
Reading Assignment
Review: Molecular Biology of the Cell and
Central Dogma
Brown Ch.1:Genomes Transcriptomes and Proteomes
Discussion in lieu of lab (in OH 203)
Personal Genomics Reading packet (BB Readings)
M 9/7
Labor Day, No Class
W 9/9
DNA Replication
DNA Mutation
Brown Ch. 15: Genome Replication
Brown Ch. 16: Mutations and DNA Repair
T 9/10
OH322
Human SNPs Lab:
Isolate DNA and PCR amplify the CDK3 gene
Brown 2.3: PCR
Lab Handouts (BB Labs: Human SNP Project)
M 9/14
EXAM
Th 9/17
OH322
Human SNPs Lab:
Restriction Digest and Sequencing Prep
Brown 2.1: Enzymes and Restriction Digests
Lab Handouts
Eukaryotic Genome Structure
Brown 7: Eukaryotic Nuclear Genomes
Brown Ch. 17: Recombination
Methods in Genomics:
DNA Sequencing, Assembly
Blast algorithm
Brown 4.1: Methodology of DNA Sequencing
Brown: 4.2: Assembly
Zvelebil, Ch. 4: Producing & Analyzing Sequence Alignments
Th 9/24
SciVis
Human SNPs Lab:
Analyze Sequences & Explore SNP Databases
Lab Handouts
M 9/28
Eukaryotic Genome Evolution
Whole Genome Duplication
Brown 18: How Genomes Evolve
Two Rounds of Whole Genome Duplication: Dehal
W 9/23
In-class GCI
MSLQ
In class essay
DNA replication and mutation, continued
W 9-16
M 9/21
Major Assigns
Introduction to Genomics 244
What is Genomics?
Is Biology an Information Science?
W 9/30
Microbial Genome Structure
Microbial Genome Evolution
Th 10/1
Pathogenomics Lab
Exam 1
Brown: Ch. 8: Prokaryotic Genomes
Genes Lost and Genes Found: Moran
Brown 2.2: DNA Cloning
SNP Paper
Example class schedule
OH322
M 10/5
Bacterial Transformation
Lab Handouts: (BB Labs: Pathogenomics)
Pathogenic microbes and virulence transfer
Reading TBA
W 10/7
Human Gut Microbiome
Ecological Microbial Communities
Human Microbiome Paper
Ecological Communities Paper
Th 10/8
SciVis
Pathogenomics Lab
Comparative Genomics of Pathogenic E. coli
Pathogenic E. coli reading
M 10/12
EXAM
Exam 2
Anatomy of Transcriptomes
Clark, Chapter 6: Transcription of Genes
Clark, Chapter 7: Protein Structure and Function
Clark, Chapter 8: Protein Synthesis
Th 10/15
SciVis
Bioinformatics Lab
Gene and Genome Annotation
Lab Handouts (BB Labs: Gene Annotation)
M 10/26
Global Decline in Coral Reef Ecosystems: Taking
a Genomics Approach
Selected papers
W 10/28
Comparative Genomics: Why study Aiptasia -- it’s
not a coral! Why study cnidarians at all?
Selected papers
Th 10/29
OH313
Aiptasia Genomics Research Project:
Intro to Research Methods
Invertebrate Biology Textbook Chapter: Cnidarians
Dinoflagellate Biology Reading
Studying transcriptomes of non-model organisms
Selected papers
W 10/14
M 11/2
W 11/4
Brainstorming on questions and methods
Genome Explorer
Th 11/5
SciVis
Aiptasia Genomics Research Project
Bioinformatic Analyses on Genome Explorer
M 11/9
W 11/11
Th 11/12
Group Meetings
Group Meetings
Projects, continued
Pathogenomics
Paper
(Take home quiz
handed out)
Take home quiz
due
Example class schedule
M 11/16
W 11/18
Th 11/19
M 11/23
W11/24
Genome Wide Gene Expression:
Arrays and Expression-by-Sequencing
Reading TBA
“Omics” – Proteomics and Interactomics
Reading TBA
Projects, continued
“Omics” – Metabolomics and Synthetic Bio
Reading TBA
Genome-Wide Association Studies
Reading TBA
Aiptasia
Genomics
Manuscript
THANKSGIVING
M 11/30
W 12/2
Th 12/3
Main Circle
M 12/7
Book Discussions
Genomics Research at Cold Spring Harbor Labs
Field Trip to Cold Spring Harbor Lab
Leave campus at 11:00, return by 6:30pm
The Making of the Fittest (Sean Carroll) -- OR –
The Genome War (James Shreeve)
TBA
CSHL
Assignment
Field Trip
Thinking Genomically: Structure and Function
T 12/8
SciVis
Today is Thursday Lab
Aiptasia Genomics Project Presentations
W 12/9
No class because today is Friday!
Final Exam (Exam 3, non comprehensive)
Time and Place TBA
Aiptasia
Genomics
Presentations
Final Exam